MmuINT1007507 @ mm10
Intron Retention
Gene
ENSMUSG00000048126 | Col6a3
Description
collagen, type VI, alpha 3 [Source:MGI Symbol;Acc:MGI:88461]
Coordinates
chr1:90768324-90773050:-
Coord C1 exon
chr1:90772952-90773050
Coord A exon
chr1:90768489-90772951
Coord C2 exon
chr1:90768324-90768488
Length
4463 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TTCTCCTCTTGCTCCTGTAGATA
3' ss Score
11.01
Exon sequences
Seq C1 exon
AGAAAACCCAGCCTCCACCTCTTCAGGCAGCACACCGAGCATCCAGTTCAACCATCAACCTCATGGTGAACACAGAACCATTGTTTCTCACTAAAACAG
Seq A exon
GTAAGTCGTGGCAGTACTAGGTCCCCTAATGGACTTCAGAAAGCATTCTGAGACCAGGGAGAAGTACTGCTTAATGGCTTGCAAACCCTTTGAAATTGAGGCCACCTGCCTGAGACTAAATCACATGACTTCCATGGGATCAGTTCCAAAGGGGTCCTCAGCTGCTGGGTTTCATCTCACTCTACATGGTCTTGGTTTCAAAAGCAGAGGAACCAAGCTTGTCACCATAGTGTTAGAAGAAGCTGGCTGGAGCTGCTTCTGAGCCCATGGCTATTATGCACGGCTCCACCAGTCACTTCCTCTGTGTTATGTTGAAACTGGCTAGGGTTGACTTGTGGTCTGTAGTGCTGCAAAGAATAAAGTTTCATTCACTTACCGAGTCATCTATAAGACACTGCTTAGGAGACCCAAGGTAACCAGACTGGATCCTGCAGAACATGTGGATTCAGATATATTTTCAGTTCTCAAAATGCCACATCTAGGCTTGGTCTTGTATTCCACTTTCCTGGATACCTGAGCACAGAGTGTGTCTGTTAGTGACAGGAAAGATTGCTGTTTTTGGGATACAAGTCTGAGAACCTGTAACCCTCCCTCCCTCTATATAAGTTGCTTTTCTATTGCTATGACATGTTCTTGTCATGTGGTCACTTGGTCATGACCAAGGCAACTTATAGAAGAAAGAGTTTATTTTGGGGGTCACAGTTCCAGAGGAATAAGGGTCTGTGATGATGGAACAGAGGTAGGAGGCTGCAGGCAGCTGGAGTAGCAGAGAGATCCTATCATGATCCACAAACAAGGGGCTTAGAACTCATTGGGGCTGATGGAAGGCTTTTAAAGCTTGAAAGCTTACCCGTGACACACCTTCTCCAGCAAGACCATACCTCCTAATCTCTCCTGAGCAACCGGGGACTGTCTTAGGCTGGGTTACTGTTGCTGTGATGAAACACCATGACCAAAGCAACTTGGAGAGGAAAGGCTTTATTGGGCTCACGCTTCCATATCACTGTTCATCACCAAAGGAAGTCGGGACAGGAACTCAAACAGGGCAGGAACCTGGAGTCAAGAGCTGATGCAGAGACCAGGGAGAAGTACTGCTTAATGGCTTGCTCCCTATGCATGGCTTGCTCAGCCTGCTTTCTTATAGAACCCAGAACCACCAGCCCAGGGATGGCACCACCTATAATGGGATTGCCCTCCACCATCAATCACTAATTAAGAAAATGCCCTACAGGCCTGCCTACAACCCAATCTTATAGCGGCATTTTCTTACTTGCAGTTCCCTCCTCTCAGATGACTTCAGCTTGTGTCAAGTTGTCCCAAAACTAGCCAGACCAGGGACCAAACACATGTTCAAATATTTGAGCCAATGGGAGCCATTCACATTCACATAACACTTTCATTTAGCAGAATGGAGGCTTGGCTAACTAGCTTTGAGGAAGTGACTACACAGTGATCAATTTGTTTGACTTAGGCACCAAAGGCGCCATTAACTGACATGAGAACTCAAAATCCTGTGAGACTTTAGTTATGGTACTGTTTCATAGTCCTCAGAGTGCAAGCCCCTGCTTAGCATGGAGATTGTCTGATGCCTTCTGGCCAGTCAGGAGGAACAGGATGCCTCTCAATACGTGCTTTCTTTCTGAGTCATCATTCATAAGCAGCCTTTGTAACTGCCTTTGTAACTGTACTAGACGGAAGAGCTACTACCATTGTCATTTAACAGCAAGCGACTGCATGGTGTCCAATGTCTCTAGCCTTTCCTGTGAAAGGCTAGCAGAAGAATAGGGAGTTTTTCCAATAGAAATTTTTGGGACTGAGGGAGGTGGGGCTCCATACAGGTGGTGGTAATTAACTACAACTGCTGAGAGATTCTATAAAAAGCCTTGAAGAAATTTAATGCTATGGTGTAAATGCAAACTGGAAAAGTGAAGTAGGTGGGTGAAGTGAGAGTTGGTTGGGGGAGGGGGAGGAGGGAGAGGAGGAGGGGGAAGAGGAAGGAGGAGAAGAGGAAGGAGGAAGAAGAGGGAGGAGGGAGGAAGGGGAGGAGGTAGAGGAGGCGGGGGAGGAGACGCCACTGCTCATCAGTTTCTGCTGTCCACACCAAAGACTACAGACAGACTTTTGTCTCCTGCCTGGTTCTACCCTGCAGCTCACAGTCTATTCTGGTCTATTCTTAAGCCACCATGGTAAGGATGCCCCAACATGAATGCTGACCTCAAAAGAAAGCCACATCTCTGTGGCTGGGGTTTTCTTGGATTTTCCTTCAAGATACTGTCACAGGGTCAGGGAGATTGCTCAGTGGGTAAAGCACCAAGGGTGTAAGCTTGAGAACCCAAGTTTGAACCCCAGAGCCCCTGTAAATGCGGAAAGAGAGAATCAACTTCACAACATTTGCCTTTGACTGCCAAACTCATGCCACGGCCCACCCCTCTCCTGTCATGTTCCCATGCACAATAACAAGTAAAATTAGGGGAAAAAAACCCCCAAAACCAAACACCAGCCAAAGAAGACCCAGAATACATTCACTTCAAAGACACAGAAAGCTGTGTGTTTAATCTGATTCCCTCTTCCTAGCTTTCGTCTCTGAGTATGGAAAATGTAAAATTTCCAGCAAACTCTTGTTTCATTGAGAGACTTGGAGGAACTCCTAGACAGCAAGATTCAGGGATAAGTTGGTTTCTTTATGTGTGCCGCTGAAGGCTGAGACTGTATAAACAGTGTTTAGTTAGCGTAAACAACATAATCTTTAAACACTAATCTGGGTCAGGCTGTTCTGTTTTTAAATGTGGAGTTGCTGCTTCCAGAATCAGGGAAGGATTTTCTCCACAGACATGTAACACTGTCTGACAAAGAGGGGAGATTTGGGTTTTGTTTGTAACGGGGACCCACGTTCCTGTCAAGGCCGCAGAGCATTTGTTTGCGGGTGAATCTAAAATCTGTCTCCTTCCCACTGATGGTGGTGAGGTAGTCTGAGGATGCAGGTGAATGTCTGTGTCTTCTTGACAAAGCCCGACAAGGGCAGAGGAGTCTGACTCCATGTCTCCCAGCTCAAGCGTGTCCTTTTGCTAGAGAACTGTGCTTCCAGAAGACCCTGCCTCGAGGTGAAGGTTGATTCTGCTGGTAGACCTCCAACAGCATCCACACCTTGCCTTTCAAGGCTCTAGACTTTGCAGCATTACGTTTGAAATGGTTAGAATTTGTATTTTGAAAACCAAGCAAAGCAAACCTTCCTTAAAATCTCCACTTTACCCTTTGCTTCCCTTAGCTCTCAAATATTACAATGCAGCCACTTTTAAGTAGTAAGGTTACTGTCTATTAAAGCCACTTAGCAACGACTGAACAAGTCCTTCAGTATTGTCTTACTCGAGGAAAGCAAGGAGGGCGCTTTGTGAGGGAGAGCCTTGAGTCAGGTTGGTAGCCACTCCCACAAACGTGCAGATTATCTGATCCTGAGCCTTTGTTGAAAGAAGGCTTAGACTTTCAGACTTCTAGATTAAAACATTTTACATGCACACGTCTTTCCCAGCAAACTCCAGCGTTTGCCAGAAAGTTCTGTAAACAGAAGTCTTGCTGTTCTCAAACTGTCAATTTACCTCTGTAGGCATCTAGGGGACCCAGCCTTATTTTGCAACTGGGCTCCAGCAGGCGTGTGCATTCAAACCCTGAACTTCCTTAACTGGAGACAAACCAAGCTTCTGGCCCCCACAAAGTCTTGCCCTGGGGCATTTCTGCGGCCTGAGGAGCTTCTTCTCCATCTTAGTTTTATGTGAGAGGGAAGAAAAGTAGTCGGCTATACTGTATCTGCACACACACTTAACACGATGAACATCTGTTGAAGGCCTGGCGAGAAGGCCTGGTGGTTAAGAGTGGTTGCTGATCTTGCAGGGGTCAGAGGTCAGTGCTAGCACCCATGTTAGGCTGCTCACAACTGCCTCTGACTCTAGCTCTAGGGGAACTGACATAGAACACAAGCATAAACAATAAAGTGTATATATTTACTTTTATTTTTATTTACTTTTTTTCAAAAAAGAATACTCAATTACAATTTACATACATTTTCAATCTACTTATCTTCTTGAAATGTATAGTCTAACAGAATTTAATGCTATTTACCAAGGAGTATGAAAGTCCATGGTCTGGACAGTGTAGACAGAAAGAACTGGAGAGCAGATGACCTCAAAATTGAAATGGGGAGAAGTTAGTCATTTTATTTTTGTTATTCAGTGACAGCTAATAGTTGAGATTCTTGCTGTACTTTTTGTTTATTCTTTGCAAACCTGTGACTGACTGCTATGTCAGTTTAATAATGAAGAAACAGAGGCTCGGGTAGGTTAAAACCTTCCCACCAGGAAATTCTTCTCTACAGTAGCATTGAGATCCAACCACAGACTCCAATATGGAGTCTGGAGGCTGAGGCGTTGGCACAAACCTACTGATGCTCCTTTCTCCTCTTGCTCCTGTAG
Seq C2 exon
ATATATGTAAGCTGTCCAGAGATGCTGGGACTTGTGTGGACTTCAAGTTACTATGGCACTATGACCTAGAGAGCAAAAGTTGCAAGAGATTCTGGTATGGAGGTTGTGGAGGCAACGAGAACAGATTCCACTCCCAGGAAGAATGTGAAAAGATGTGTAGTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048126:ENSMUST00000097653:39
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.245 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001418=Kunitz_BPTI=WD(100=94.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types